Merge pull request #91 from bcgsc/bugfix/DEVSU-2793-remove-kbvar-match-when-no-stmt

Bugfix/devsu 2793 remove kbvar match when no stmt

Author: elewis2

pori_python/ipr/ipr.py

@@ -168,6 +168,7 @@ def convert_statements_to_alterations(
         diseases = [c for c in statement["conditions"] if c["@class"] == "Disease"]
         disease_match = len(diseases) == 1 and diseases[0]["@rid"] in disease_matches
         reference = ";".join([e["displayName"] for e in statement["evidence"]])
+
         if statement['relevance']['name'] == 'eligibility':
             reference = ";".join([e["sourceId"] for e in statement["evidence"]])
 
@@ -624,6 +625,20 @@ def get_kb_matches_sections(
     kb_statement_matched_conditions = get_kb_statement_matched_conditions(
         gkb_matches, allow_partial_matches
     )
+
+    if not allow_partial_matches:
+        # remove kb_matches that are not part of any fully matched condition set
+        unique_kb_variant_ids = list(
+            set(
+                [
+                    item['kbVariantId']
+                    for conditionSet in kb_statement_matched_conditions
+                    for item in conditionSet['matchedConditions']
+                ]
+            )
+        )
+        kb_variants = [item for item in kb_variants if item['kbVariantId'] in unique_kb_variant_ids]
+
     return {
         "kbMatches": kb_variants,
         "kbMatchedStatements": kb_matched_statements,

pori_python/ipr/main.py

@@ -467,9 +467,6 @@ def ipr_report(
         gkb_matches = [Hashabledict(match) for match in custom_kb_match_filter(gkb_matches)]
         logger.info(f"\t custom_kb_match_filter left {len(gkb_matches)} variants")
 
-    # KEY ALTERATIONS
-    key_alterations, variant_counts = create_key_alterations(gkb_matches, all_variants)
-
     # GENE INFORMATION
     logger.info("fetching gene annotations")
     gene_information = get_gene_information(graphkb_conn, sorted(genes_with_variants))
@@ -514,6 +511,10 @@ def ipr_report(
         gkb_matches, allow_partial_matches=allow_partial_matches
     )
 
+    # KEY ALTERATIONS
+    # must do after pruning of kbMatches for kb_matched_sections
+    key_alterations, variant_counts = create_key_alterations(gkb_matches, all_variants)
+
     # OUTPUT CONTENT
     # thread safe deep-copy the original content
     output = json.loads(json.dumps(content))

tests/test_ipr/test_data/expression.short.tab

@@ -25,3 +25,4 @@ KLHL25	27.39	outlier_high	increased expression	100.0	6.97	46.01	100.0	210.66		8.
 ZNRF3-IT1	0.2	no_category								6.75	0.12	34	-1.816	2.225	-2.505	1.744	26	0.623	-1.272	0.2	0.3	0.4	0.5
 PTP4A3	1.33	high_percentile	increased expression	100.0	9.74	99.62	100.0	32.2		6.09	-2.217	87	1.863	2.013	0.286	-0.767	66	-0.091	-1.824	0.2	0.3	0.4	0.5
 ERBB2	0.05	no_category		67.0	0.62	51.71	100.0	1.01		4.8	-0.551	61	-2.009	-2.216	0.147	-2.385	86	2.299	-0.953	0.2	0.3	0.4	0.5
+DPYD	1.12	increased rna expression	increased expression	97.0	4.75	73.38	100.0	50.19		0.99	-0.193	92	2.786	0.537	2.113	1.888	31	0.915	0.861	0.2	0.3	0.4	0.5

tests/test_ipr/test_ipr.py

@@ -10,6 +10,7 @@
     get_kb_matched_statements,
     get_kb_statement_matched_conditions,
     get_kb_variants,
+    get_kb_matches_sections,
 )
 from pori_python.types import Statement
 
@@ -696,9 +697,12 @@ def test_partial_matches_omitted(self):
         for item in input_fields:  # we don't care about these for this test
             item["variantType"] = "test"
             item["kbVariant"] = "test"
+
         gkb_matches = create_gkb_matches(input_fields)
-        stmts = get_kb_matched_statements(gkb_matches)
-        kbcs = get_kb_statement_matched_conditions(gkb_matches)
+        sections = get_kb_matches_sections(gkb_matches, allow_partial_matches=False)
+
+        stmts = sections['kbMatchedStatements']
+        kbcs = sections['kbStatementMatchedConditions']
         assert len(stmts) == 2
         assert len(kbcs) == 1  # X only
         assert kbcs[0]["kbStatementId"] == "X"
@@ -748,6 +752,53 @@ def test_partial_matches_omitted_even_when_var_used_elsewhere(self):
         assert len(kbcs) == 2  # X and Z but not Y
         assert "Y" not in [item["kbStatementId"] for item in kbcs]
 
+    def test_kbvariants_removed_from_set_when_not_part_of_full_conditionset_match(self):
+        """When there is a variant that fulfills one part of a statement's condition set,
+        but isn't part of any fully satisfied condition set,
+        the kbvariant record should be removed from the kbvariants list
+        """
+        input_fields = [
+            {
+                "variant": "A",
+                "kbVariantId": "test1",
+                "kbStatementId": "X",
+                "requiredKbMatches": ["test1", "test2", "test3"],
+            },
+            {
+                "variant": "B",
+                "kbVariantId": "test2",
+                "kbStatementId": "X",
+                "requiredKbMatches": ["test1", "test2", "test3"],
+            },
+            {
+                "variant": "A",
+                "kbVariantId": "test1",
+                "kbStatementId": "Y",
+                "requiredKbMatches": ["test4", "test1"],
+            },
+            {
+                "variant": "D",
+                "kbVariantId": "test4",
+                "kbStatementId": "Y",
+                "requiredKbMatches": ["test4", "test1"],
+            },
+        ]
+        for item in input_fields:  # we don't care about these for this test
+            item["variantType"] = "test"
+            item["kbVariant"] = "test"
+        gkb_matches = create_gkb_matches(input_fields)
+        sections1 = get_kb_matches_sections(gkb_matches, allow_partial_matches=False)
+        kbcs1 = sections1['kbStatementMatchedConditions']
+        kbvars1 = sections1['kbMatches']
+        assert len(kbcs1) == 1  # only fully matched condition sets included
+        assert len(kbvars1) == 2  # therefore, kbvars associated with stmt X are pruned
+
+        sections2 = get_kb_matches_sections(gkb_matches, allow_partial_matches=True)
+        kbcs2 = sections2['kbStatementMatchedConditions']
+        kbvars2 = sections2['kbMatches']
+        assert len(kbcs2) == 2  # all condition sets included
+        assert len(kbvars2) == 3  # therefore, no pruning
+
     def test_partial_matches_included(self):
         """check statements that are only partially supported
         are included when allow_partial_matches=True"""